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[bioontology-support] REST query with a slash in the search string

Marco Brandizi brandizi at ebi.ac.uk
Thu Dec 8 13:18:31 PST 2011


Hi Paul, Trish, thank you very much for your reply.

Unfortunately I am not in control of that URL, cause I'm coming at it 
through OntoCAT. I'll forward this to their authors.

Cheers,
M.


On 08/12/2011 19:54, Paul R Alexander wrote:
> Marco,
>
> There's a known bug in our server software (Apache Tomcat) that 
> prevents the use of encoded slashes in the URL proper. However, you 
> can pass them in query string parameters just fine. The URL below does 
> this:
> http://rest.bioontology.org/bioportal/search/?query=Mutant+%2F+Wild+type+comparison_design&maxnumhits=10000000&level=1&includeproperties=0&isexactmatch=1&ontologyids=1136&subtreerootconceptid=efo%3AEFO_0003740&apikey={YourAPIKey}
>
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
>
>
> On 12/8/11 10:38 AM, Trish Whetzel wrote:
>> Hi Marco,
>>
>> The issue is not with the "/" character. We worked with the Rat 
>> Genome Database folks and their Rat Strain Ontology has a lot of 
>> interesting characters that we tested the search with so strings like 
>> "DA.F344-Aia1/1" can be used with the Search, url-encoded of course. 
>> E.g. 
>> http://rest.bioontology.org/bioportal/search/?query=DA.F344-Aia1%2F1&apikey={YourAPIKey}. 
>> <http://rest.bioontology.org/bioportal/search/?query=DA.F344-Aia1%2F1&apikey=%7BYourAPIKey%7D.> 
>> At best I can see right now is that there might be a problem with the 
>> search within subtree.
>>
>> Trish
>>
>> PS - I don't think the Search call takes the param "level"
>>
>>
>> On Dec 8, 2011, at 11:52 AM, Marco Brandizi wrote:
>>
>>> Hi all,
>>>
>>> sorry if the following question has already been asked, I cannot 
>>> find a reference to this. Bioportal REST seems to fail when it gets 
>>> a string with a slash character in it, for instance this:
>>>
>>> http://rest.bioontology.org/bioportal/search/Mutant+%2F+Wild+type+comparison_design/?maxnumhits=10000000&apikey=<my-key>&level=1&includeproperties=0&isexactmatch=1&ontologyids=1136&subtreerootconceptid=efo%3AEFO_0003740
>>>
>>> which I'm trying to use to see if there is 'Mutant / Wild type 
>>> comparison_design' under the tree rooted at EFO_0003740, instead 
>>> tells me a 404/Not Found, which I interpret as the inability to 
>>> recognise that the %2F (note it's escaped) is part of the search string.
>>>
>>> Is there any massaging/escaping/etc I can do to the input to make it 
>>> working?
>>>
>>> Thanks in advance for any help.
>>>
>>> -- 
>>>
>>> ===============================================================================
>>> Marco Brandizi, PhD<brandizi at ebi.ac.uk <mailto:brandizi at ebi.ac.uk>>
>>>
>>> Microarray Group - Sr Software Engineer
>>> http://www.ebi.ac.uk/microarray
>>>
>>> European Bioinformatics Institute
>>> Hinxton, CB10 1SD, United Kingdom
>>> Office A3141
>>>
>>> Tel.: +44 (0)1223 492 613
>>> Fax: +44 (0)1223 492 620
>>>
>>> http://www.marcobrandizi.info
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> http://www.bioontology.org
>>
>> Now on Twitter: http://twitter.com/#!/bioontology 
>> <http://twitter.com/#%21/bioontology>
>> and "Like" us on Facebook: 
>> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-- 

===============================================================================
Marco Brandizi, PhD<brandizi at ebi.ac.uk>

Microarray Group - Sr Software Engineer
http://www.ebi.ac.uk/microarray

European Bioinformatics Institute
Hinxton, CB10 1SD, United Kingdom
Office A3141

Tel.: +44 (0)1223 492 613
Fax: +44 (0)1223 492 620

http://www.marcobrandizi.info

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